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JAL-3829 patch failing tests and todo for future
author
Jim Procter
<j.procter@dundee.ac.uk>
Sat, 11 Sep 2021 10:53:05 +0000
(11:53 +0100)
committer
Jim Procter
<j.procter@dundee.ac.uk>
Sat, 11 Sep 2021 10:53:05 +0000
(11:53 +0100)
src/jalview/jbgui/GStructureChooser.java
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test/jalview/gui/StructureChooserTest.java
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test/jalview/gui/structurechooser/StructureChooserQuerySourceTest.java
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diff --git
a/src/jalview/jbgui/GStructureChooser.java
b/src/jalview/jbgui/GStructureChooser.java
index
50c9a2e
..
2a6c1f2
100644
(file)
--- a/
src/jalview/jbgui/GStructureChooser.java
+++ b/
src/jalview/jbgui/GStructureChooser.java
@@
-88,7
+88,7
@@
public abstract class GStructureChooser extends JPanel
{
private static final Font VERDANA_12 = new Font("Verdana", 0, 12);
{
private static final Font VERDANA_12 = new Font("Verdana", 0, 12);
- protected static final String VIEWS_FILTER = "VIEWS_FILTER";
+ public static final String VIEWS_FILTER = "VIEWS_FILTER";
protected static final String VIEWS_FROM_FILE = "VIEWS_FROM_FILE";
protected static final String VIEWS_FROM_FILE = "VIEWS_FROM_FILE";
diff --git
a/test/jalview/gui/StructureChooserTest.java
b/test/jalview/gui/StructureChooserTest.java
index
685e1bc
..
dbe0906
100644
(file)
--- a/
test/jalview/gui/StructureChooserTest.java
+++ b/
test/jalview/gui/StructureChooserTest.java
@@
-163,10
+163,8
@@
public class StructureChooserTest
@Test(groups = { "Functional" })
public void fetchStructuresInfoMockedTest()
{
@Test(groups = { "Functional" })
public void fetchStructuresInfoMockedTest()
{
- Assert.fail("Not yet implemented");
TDBeaconsFTSRestClientTest.setMock();
TDBeaconsFTSRestClientTest.setMock();
-
- // PDBFTSRestClient.setMock();
+ PDBFTSRestClient.setMock();
SequenceI[] selectedSeqs = new SequenceI[] { upSeq };
StructureChooser sc = new StructureChooser(selectedSeqs, seq, null);
sc.fetchStructuresMetaData();
SequenceI[] selectedSeqs = new SequenceI[] { upSeq };
StructureChooser sc = new StructureChooser(selectedSeqs, seq, null);
sc.fetchStructuresMetaData();
diff --git
a/test/jalview/gui/structurechooser/StructureChooserQuerySourceTest.java
b/test/jalview/gui/structurechooser/StructureChooserQuerySourceTest.java
index
59c4a50
..
414e8a7
100644
(file)
--- a/
test/jalview/gui/structurechooser/StructureChooserQuerySourceTest.java
+++ b/
test/jalview/gui/structurechooser/StructureChooserQuerySourceTest.java
@@
-45,6
+45,7
@@
import jalview.fts.core.FTSRestResponse;
import jalview.fts.service.pdb.PDBFTSRestClient;
import jalview.fts.threedbeacons.TDBeaconsFTSRestClientTest;
import jalview.gui.JvOptionPane;
import jalview.fts.service.pdb.PDBFTSRestClient;
import jalview.fts.threedbeacons.TDBeaconsFTSRestClientTest;
import jalview.gui.JvOptionPane;
+import jalview.gui.StructureChooser;
import jalview.jbgui.FilterOption;
public class StructureChooserQuerySourceTest
import jalview.jbgui.FilterOption;
public class StructureChooserQuerySourceTest
@@
-261,11
+262,16
@@
public class StructureChooserQuerySourceTest
FTSRestResponse upResponse = null;
FTSRestResponse pdbResponse = null;
FTSRestResponse upResponse = null;
FTSRestResponse pdbResponse = null;
-
+ // TODO test available options
+ // Best coverage
+ // Best Alphafold Model
+ // Best model (by confidence score)
+ // Will also need to develop a more sophisticated filtering system
+ FilterOption opt = tdbquery.getAvailableFilterOptions(StructureChooser.VIEWS_FILTER).get(0);
try {
try {
- upResponse = tdbquery.fetchStructuresMetaData(upSeq, tdbquery.getDocFieldPrefs().getStructureSummaryFields(), null, false);
+ upResponse = tdbquery.fetchStructuresMetaData(upSeq, tdbquery.getDocFieldPrefs().getStructureSummaryFields(), opt, false);
// test ranking without additional PDBe data
// test ranking without additional PDBe data
- FTSRestResponse firstRanked = tdbquery.selectFirstRankedQuery(upSeq, upResponse.getSearchSummary(), tdbquery.getDocFieldPrefs().getStructureSummaryFields(), "", false);
+ FTSRestResponse firstRanked = tdbquery.selectFirstRankedQuery(upSeq, upResponse.getSearchSummary(), tdbquery.getDocFieldPrefs().getStructureSummaryFields(), opt.getValue(), false);
assertTrue(firstRanked.getNumberOfItemsFound()<upResponse.getNumberOfItemsFound());
// NB Could have race condition here
String pdb_Query = tdbquery.buildPDBFTSQueryFor(upResponse);
assertTrue(firstRanked.getNumberOfItemsFound()<upResponse.getNumberOfItemsFound());
// NB Could have race condition here
String pdb_Query = tdbquery.buildPDBFTSQueryFor(upResponse);